Research workbench
Crystal structure of laglidadg meganuclease I-gpemi bound to uncleaved DNA
Analyse Crystal structure of laglidadg meganuclease I-gpemi bound to uncleaved DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YHX
- Type
- protein + DNA
- Length
- 348 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein 3/HOMING endonuclease-like fusion protein; DNA (27-mer)
- UniProt
- C7SQG1
- Ligands
- CA
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein 3/HOMING endonuclease-like fusion protein | protein | 294 | 50% helix, 23% strand | C7SQG1 |
| B | DNA (27-mer) | dna | 27 | — | — |
| C | DNA (27-mer) | dna | 27 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.68 | 0.89 | 26 | empty |
| 2 | 56 | 0.67 | 0.96 | 20 | empty |
| 3 | 118 | 0.54 | 0.84 | 20 | empty |
| 4 | 116 | 0.41 | 0.76 | 27 | empty |
| 5 | 60 | 0.27 | 0.74 | 10 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1630 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 1547 Ų buried · 34 hydrogen bonds · protein-nucleic
- B–C · 1362 Ų buried · 89 hydrogen bonds · nucleic-nucleic
Compared structures
- 4YHX · Crystal Structure of LAGLIDADG Meganuclease I-GpeMI Bound to Uncleaved DNA · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt C7SQG1
- Elsewhere: RCSB PDB 4YHX · PDBe 4YHX · UniProt C7SQG1
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